Habitat structural complexity in the 21st century: measurement, fish responses and why it matters Thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy School of Life and Environmental Sciences The University of Sydney Augustine Gregory Porter August 2018 i Contents Acknowledgements ................................................................................................................................ vi Author Attribution ................................................................................................................................ vii Abstract ................................................................................................................................................ viii Chapter 1: General Introduction.................................................................................................................1 Summary .................................................................................................................................................1 1.1 Habitat Structural Complexity ....................................................................................................1 1.1.1 History of marine HSC evaluation ......................................................................................2 1.1.2 HSC in the Anthropocene ...................................................................................................4 1.1.3 3D Capture ..........................................................................................................................5 1.1.4 Metrics of marine HSC ........................................................................................................7 1.1.5 Complexity as design criteria ..............................................................................................9 1.2 Fish and structural complexity ................................................................................................ 10 1.2.1 Known fish responses to HSC .......................................................................................... 10 1.2.2 Importance of functional assemblages ........................................................................... 12 1.2.3 Multi‐scale fish responses ............................................................................................... 12 1.3 Thesis aims ............................................................................................................................... 13 1.3.1 Key Questions: ................................................................................................................. 13 Chapter 2: Marine infrastructure supports abundant, diverse fish assemblages at the expense of β diversity .................................................................................................................................................... 15 Summary .............................................................................................................................................. 15 2.1 Introduction ............................................................................................................................. 15 2.2 Methods ................................................................................................................................... 18 2.2.1 Study area and design ..................................................................................................... 18 2.2.2 Data collection ................................................................................................................. 21 2.2.3 Fish Groups ...................................................................................................................... 22 ii 2.2.4 Univariate metrics ........................................................................................................... 23 2.2.5 Statistical analysis ............................................................................................................ 23 2.3 Results ...................................................................................................................................... 24 2.3.1 Univariate metrics ........................................................................................................... 24 2.3.2 Multivariate metrics ........................................................................................................ 26 2.4 Discussion ................................................................................................................................ 29 2.4.1 Functional groups ............................................................................................................ 30 2.4.2 Trophic structure ............................................................................................................. 30 2.4.3 Regional differences ........................................................................................................ 31 2.4.4 β diversity......................................................................................................................... 32 2.5 Conclusion ................................................................................................................................ 33 Chapter 3: Novel metrics of structural complexity from 3D benthic habitat data ................................. 34 Summary .............................................................................................................................................. 34 3.1 Background .............................................................................................................................. 34 3.1.1 Context ............................................................................................................................. 34 3.1.2 3D data ............................................................................................................................. 35 3.1.3 Metrics of complexity ...................................................................................................... 35 3.2 Metrics Extracted ..................................................................................................................... 36 3.2.1 Metric Validation ............................................................................................................. 40 3.3 Deriving Feature Size ............................................................................................................... 42 3.3.1 Resolution and Complexity .............................................................................................. 42 3.3.2 From Complexity loss to Object Size ............................................................................... 48 3.3.3 Object size validation ....................................................................................................... 49 3.4 Discussion ................................................................................................................................ 52 3.4.1 Conclusion........................................................................................................................ 53 Chapter 4: Exploring structural niche space in benthic habitats using 3D modelling ............................ 55 iii Summary: ............................................................................................................................................. 55 4.1 Introduction ............................................................................................................................. 55 4.2 Methods ................................................................................................................................... 58 4.2.1 Mapping ........................................................................................................................... 59 4.2.2 Data extraction ................................................................................................................ 60 4.2.3 Statistical analysis ............................................................................................................ 60 4.3 Results ...................................................................................................................................... 62 4.3.1 Structure metrics ............................................................................................................. 62 4.3.2 Distribution structure metrics ......................................................................................... 65 4.4 Discussion ................................................................................................................................ 73 Chapter 5: Structural complexity drivers of reef fish assemblages: which metrics are important? ...... 76 Summary: ............................................................................................................................................. 76 5.1 Introduction ............................................................................................................................. 76 5.2 Methods ................................................................................................................................... 78 5.2.1 Study Design .................................................................................................................... 78 5.2.2 Habitat Structural Complexity (predictor) Data .............................................................